TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene.

Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors: Kit, Kdr, Pdgfra.

Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line.

Background: Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied.

Anopheles mosquitoes reveal new principles of 3D genome organization in insects.

Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels.

Quantitative prediction of enhancer-promoter interactions.

Recent experimental and computational efforts have provided large data sets describing three-dimensional organization of mouse and human genomes and showed the interconnection between the expression profile, epigenetic state, and spatial interactions of loci. These interconnections were utilized to infer the spatial organization of chromatin, including enhancer-promoter contacts, from one-dimensional epigenetic marks. Here, we show that the predictive power of some of these algorithms is overestimated due to peculiar properties of the biological data.

C-InterSecture-a computational tool for interspecies comparison of genome architecture.

Motivation: Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison.

Results: To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species.